My main concern is that when the suspension compresses, assuming a 3" coil-over stroke, the axle and hence the shock mount, should move rearward about 1" (based on my suspensions geometry, may be different on yours). So, because the lower shock mount moves forward and backward, but the upper mount does not move, the shock will have to tilt to compensate...

Are the shock bushings just designed to deform enough to allow the shock to tilt?

Should I just position the upper shock mount crossmember so that the shock is perfectly perpendicular to the upper and lower shock mounts(forward and backward -- I know side to side the shock can angled) at ride height?